Sat Oct 8 11:37:54 PDT 2011 #!/bin/csh -f # input: # $1 receptor coordinates file; # $2 grid size; # $3 # of iterations for the first run; # $4 # of iterations for the second run; # $5 # of iterations for the third run; # output: # delphi map: $1.phi # log file: delphi.out set RECCRG = rec+sph2.crg set GRID = 179 set n1 = 50 set n2 = 120 set n3 = 180 set DELPHI = $DOCK_BASE/private/delphi set VDW = vdw.siz #set VDW = vdw.hydren set CRG = amb2.crg.oxt set PRM = genric.prm # three step focussing calc. if (-e ARCDAT) /bin/rm ARCDAT cp $VDW fort.11 cp $CRG fort.12 cp $RECCRG fort.13 echo "gsize=$GRID, perfil=20, bndcon=2, linit=$n1\n" >! fort.10 cat $PRM >> fort.10 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=60, bndcon=3, linit=$n2\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=90, bndcon=3, linit=$n3\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) /bin/rm fort.1[0-3] fort.18 ARCDAT mv fort.14 $RECCRG:r.phi ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sat Oct 8 2011 at 11:37:54 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4461 !!! WARNING: HIQ 440 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5627658 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : dipolar x,y,z periodic bc. flags : F F F # of linear iterations : 50 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 20.00000 xmin,xmax (A): -28.78800 34.47100 ymin,ymax (A): 34.51100 95.41400 zmin,zma (A): 31.42300 89.17000 x,y,z range (A): 63.25900 60.90300 57.74699 scale (grids/A): 0.5627658 object centre (A): 2.841500 64.96250 60.29650 number of atom coordinates read : 4461 total number of charged atoms : 4302 net assigned charge : -5.485957 assigned positive charge : 674.0192 centred at (gu) : 91.59831 89.61694 89.20635 assigned negative charge : -679.5082 centred at (gu) : 91.52845 89.72694 89.37289 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 8881 nv = 96 ne = 84 npr = 94150 no. pairs analyzed = 94150 no. exposed pairs = 5068 no. arc points = 34346 no. surface atoms = 1717 nbur = 2744 mkacc time = 0.2400000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 360 mr = 5098 m= 2 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 118 time to turn everything in is 0.4600000 number of dielectric boundary points 4122 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3569 ## 435 charges are in solution ## iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 11856 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.8511928E-09 -3.1898471E-09 midg,1,midg; midg,igrid,midg 1.4551284E-09 -2.5306632E-09 1,midg,midg; igrid,midg,midg -1.3732517E-09 8.9474761E-10 gauss-seidel spectral radius is 0.9838133 estimated iterations to convergence 65 setup time was (sec) 0.7600000 now iterating at: 11:37:55 rms-change max change #iterations 0.1081352 15.97139 at 10iterations 8.2333274E-03 1.136280 at 20iterations 8.2227268E-04 0.1077213 at 30iterations 1.8041040E-04 2.6051283E-02 at 40iterations 5.8892929E-05 9.3151331E-03 at 50iterations finished qdiffx linear iterations at : 11:37:59 total time elapsed so far: 4.460000 # loops : 50 mean,max change (kT/e) : 5.8892929E-05 9.3151331E-03 energy calculations done at 4.460000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.630000 DelPhi exited at 11:37:59 4.631u 0.424s 0:05.34 94.5% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sat Oct 8 2011 at 11:37:59 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4461 !!! WARNING: HIQ 440 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.688297 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 120 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 60.00000 xmin,xmax (A): -28.78800 34.47100 ymin,ymax (A): 34.51100 95.41400 zmin,zma (A): 31.42300 89.17000 x,y,z range (A): 63.25900 60.90300 57.74699 scale (grids/A): 1.688297 object centre (A): 2.841500 64.96250 60.29650 number of atom coordinates read : 4461 total number of charged atoms : 4302 net assigned charge : -5.485957 assigned positive charge : 674.0192 centred at (gu) : 94.79365 88.84965 87.61765 assigned negative charge : -679.5082 centred at (gu) : 94.58495 89.18028 88.11828 start vw surface at 0.1500000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 99339 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34346 grid for indexing accessible points = 1.400000 m= 32724 mr = 71643 m= 3757 mr = 23874 m= 112 mr = 2142 m= 2 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.4100000 no. cavity mid-points inaccessible to solvent = 6242 time to turn everything in is 0.7700000 number of dielectric boundary points 38263 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 358 iepsmp to db, and charging done at 0.9400000 number of grid points assigned charge 33156 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 0.5627658 object centre at (A) : 2.841500 64.96250 60.29650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.3938669E-02 -2.2219365E-02 midg,1,midg; midg,igrid,midg 1.3456389E-02 -1.6521057E-02 1,midg,midg; igrid,midg,midg -1.0278151E-02 1.8487263E-02 gauss-seidel spectral radius is 0.9984317 estimated iterations to convergence 200 setup time was (sec) 1.130000 now iterating at: 11:38:01 rms-change max change #iterations 4.571511 161.4569 at 10iterations 2.025651 61.66645 at 20iterations 0.9025349 29.64166 at 30iterations 0.3986432 12.60588 at 40iterations 0.1776710 5.027336 at 50iterations 7.9134561E-02 2.071529 at 60iterations 3.5262510E-02 0.9438972 at 70iterations 1.5704842E-02 0.5133934 at 80iterations 7.0016030E-03 0.1961870 at 90iterations 3.1426118E-03 9.2716217E-02 at 100iterations 1.4280668E-03 4.2907715E-02 at 110iterations 6.5830216E-04 1.9109726E-02 at 120iterations finished qdiffx linear iterations at : 11:38:11 total time elapsed so far: 10.71000 # loops : 120 mean,max change (kT/e) : 6.5830216E-04 1.9109726E-02 energy calculations done at 10.71000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.88000 DelPhi exited at 11:38:11 10.888u 0.465s 0:11.84 95.7% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sat Oct 8 2011 at 11:38:11 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4461 !!! WARNING: HIQ 440 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.532446 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 180 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 90.00000 xmin,xmax (A): -28.78800 34.47100 ymin,ymax (A): 34.51100 95.41400 zmin,zma (A): 31.42300 89.17000 x,y,z range (A): 63.25900 60.90300 57.74699 scale (grids/A): 2.532446 object centre (A): 2.841500 64.96250 60.29650 number of atom coordinates read : 4461 total number of charged atoms : 4302 net assigned charge : -5.485957 assigned positive charge : 674.0192 centred at (gu) : 97.19020 88.27409 86.42612 assigned negative charge : -679.5082 centred at (gu) : 96.87730 88.77030 87.17728 start vw surface at 0.1700000 fill in re-entrant regions at 0.6500000 boundary points on vw surface= 231046 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34346 grid for indexing accessible points = 1.400000 m= 112280 mr = 174044 m= 34147 mr = 92064 m= 6217 mr = 26958 m= 493 mr = 4522 m= 9 mr = 263 m= 0 mr = 2 time to grow re-entrant surface = 1.220000 no. cavity mid-points inaccessible to solvent = 20484 time to turn everything in is 2.000000 number of dielectric boundary points 86339 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 22 iepsmp to db, and charging done at 2.150000 number of grid points assigned charge 34397 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 1.688297 object centre at (A) : 2.841500 64.96250 60.29650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4037429 -0.2692523 midg,1,midg; midg,igrid,midg 0.1890555 -0.2885157 1,midg,midg; igrid,midg,midg -0.1328888 0.1971947 gauss-seidel spectral radius is 0.9992275 estimated iterations to convergence 284 setup time was (sec) 2.340000 now iterating at: 11:38:14 rms-change max change #iterations 11.36259 262.3965 at 10iterations 6.578527 138.7026 at 20iterations 3.794672 93.04865 at 30iterations 2.182700 47.41448 at 40iterations 1.249556 24.39047 at 50iterations 0.7151026 14.35417 at 60iterations 0.4092911 6.606884 at 70iterations 0.2331528 3.956381 at 80iterations 0.1329862 2.373514 at 90iterations 7.5731710E-02 1.287998 at 100iterations 4.3139089E-02 0.7562828 at 110iterations 2.4620581E-02 0.3862762 at 120iterations 1.4031146E-02 0.2517471 at 130iterations 8.0042779E-03 0.1189117 at 140iterations 4.5967372E-03 8.0072641E-02 at 150iterations 2.6607413E-03 4.4769287E-02 at 160iterations 1.5622113E-03 2.6367188E-02 at 170iterations 9.3590532E-04 1.6105652E-02 at 180iterations finished qdiffx linear iterations at : 11:38:31 total time elapsed so far: 18.71000 # loops : 180 mean,max change (kT/e) : 9.3590532E-04 1.6105652E-02 energy calculations done at 18.71000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.89000 DelPhi exited at 11:38:31 18.890u 0.483s 0:19.79 97.8% 0+0k 0+0io 0pf+0w